primirTSS

primirTSS identifies miRNA transcription start sites (TSSs) from high-throughput sequencing data by integrating promoter-associated ChIP-seq signals (H3K4me3 and Pol II) with conservation scores and sequence-derived features to improve precision in miRNA TSS mapping.

Key Features:

• Integration of multi-omics data: Integrates promoter-associated ChIP-seq signals H3K4me3 and RNA polymerase II (Pol II) to enable cell-type/context-aware identification of miRNA TSSs.
• Conservation and sequence feature analysis: Incorporates conservation scores and sequence-derived features to support prediction of evolutionarily conserved transcription initiation sites.
• Flexible data input options: Operates with either H3K4me3 or Pol II ChIP-seq data alone or with both assays when available.

Scientific Applications:

• Gene regulation studies: Maps miRNA promoter usage and upstream regulatory mechanisms governing miRNA expression.
• Genetics and immuno-oncology research: Supports analysis of regulatory variation and miRNA roles in immune signaling and cancer biology.
• Transcriptional process analysis: Facilitates investigation of miRNA transcription initiation within genomic and epigenomic studies.

Methodology:

PrimirTSS integrates ChIP-seq evidence (H3K4me3 and/or Pol II) with conservation scores and sequence-derived features to infer miRNA transcription start sites. By combining epigenetic markers of active promoters with evolutionary and sequence-based signals, the method provides a multi-evidence, context-aware framework for miRNA TSS prediction.